ArticleBiophysical journal2008
M-TASSER: an algorithm for protein quaternary structure prediction.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Database-Driven Identification of Structurally Similar Protein-Protein Interfaces.Journal of chemical information and modeling · 2024Article
- Multi-domain and complex protein structure prediction using inter-domain interactions from deep learning.Communications biology · 2023Article
- Transmembrane dimers of type 1 receptors sample alternate configurations: MD simulations using coarse grain Martini 3 versus AlphaFold2 Multimer.Structure (London, England : 1993) · 2023Article
- Insights into protein-DNA interactions from hydrogen bond energy-based comparative protein-ligand analyses.Proteins · 2022Article
- AF2Complex predicts direct physical interactions in multimeric proteins with deep learning.Nature communications · 2022Article
- Computational structure modeling for diverse categories of macromolecular interactions.Current opinion in structural biology · 2020Review
- InterPep2: global peptide-protein docking using interaction surface templates.Bioinformatics (Oxford, England) · 2020Article
- Integrating ab initio and template-based algorithms for protein-protein complex structure prediction.Bioinformatics (Oxford, England) · 2020Article
- Predicting protein-peptide interaction sites using distant protein complexes as structural templates.Scientific reports · 2019Article
- Template-based protein-protein docking exploiting pairwise interfacial residue restraints.Briefings in bioinformatics · 2017Article
- HOMCOS: an updated server to search and model complex 3D structures.Journal of structural and functional genomics · 2016Article
- Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area.Scientific reports · 2016Article
- How special is the biochemical function of native proteins?F1000Research · 2016Review
- Are protein-protein interfaces special regions on a protein's surface?The Journal of chemical physics · 2015Article
- Evaluating template-based and template-free protein-protein complex structure prediction.Briefings in bioinformatics · 2014Article
- Template-based structure modeling of protein-protein interactions.Current opinion in structural biology · 2014Review
- DockRank: ranking docked conformations using partner-specific sequence homology-based protein interface prediction.Proteins · 2014Article
- Article
- Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale.Journal of proteome research · 2013Article
- Mapping monomeric threading to protein-protein structure prediction.Journal of chemical information and modeling · 2013Article
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2 authors.
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Abstract
In a cell, it has been estimated that each protein on average interacts with roughly 10 others, resulting in tens of thousands of proteins known or suspected to have interaction partners; of these, only a tiny fraction have solved protein structures. To partially address this problem, we have developed M-TASSER, a hierarchical method to predict protein quaternary structure from sequence that involves template identification by multimeric threading, followed by multimer model assembly and refinement. The final models are selected by structure clustering. M-TASSER has been tested on a benchmark set comprising 241 dimers having templates with weak sequence similarity and 246 without multimeric templates in the dimer library. Of the total of 207 targets predicted to interact as dimers, 165 (80%) were correctly assigned as interacting with a true positive rate of 68% and a false positive rate of 17%. The initial best template structures have an average root mean-square deviation to native of 5.3, 6.7, and 7.4 A for the monomer, interface, and dimer structures. The final model shows on average a root mean-square deviation improvement of 1.3, 1.3, and 1.5 A over the initial template structure for the monomer, interface, and dimer structures, with refinement evident for 87% of the cases. Thus, we have developed a promising approach to predict full-length quaternary structure for proteins that have weak sequence similarity to proteins of solved quaternary structure.
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